SNP芯片基因型填充至测序数据的策略  

Research on genotype imputation from SNP chip data to whole-genome sequence data

作　　者：李乐义[1,2,3] 邵东东[1,2,3] 丁向东[1,2,3] 张勤[1,2,3] 

机构地区：[1]中国农业大学动物科学技术学院,北京100193 [2]农业部动物遗传育种与繁殖重点实验室,北京100193 [3]国家畜禽育种工程实验室,北京100193

出　　处：《中国科技论文》2016年第12期1431-1436,共6页China Sciencepaper

基　　金：高等学校博士学科点专项科研基金资助项目(20110008110001);国家现代农业产业技术体系生猪产业技术体系资助项目(CARS-36);北京市科技计划项目(D15110004615004)

摘　　要：根据畜禽基因组信息,模拟了1条染色体测序数据、中密度和高密度SNP芯片数据。利用Beagle和FImpute将SNP芯片填充至测序数据,提出了一步法和两步法2种填充策略。结果表明,直接将中密度芯片填充至测序数据的一步法策略填充准确性较低,当公畜为参考群体时,两步法策略将后裔填充准确性由一步法时的0.691提高至0.863;当不同规模母畜为参考群体时,一步法策略下半同胞填充准确性为0.553～0.664,而两步法策略则大幅度提高到0.832～0.866。随着参考群体的增加,SNP芯片到测序数据的填充准确性可进一步提高,同样亲缘关系也有助于填充准确性提高。一步法填充策略下,Beagle填充准确性低于FImpute,但随着参考群体的扩大,差距逐步缩小,而在两步法策略下,Beagle与FImpute基因型填充准确性没有显著差异。In this paper,the sequencing data,medium and high density SNP chips of chromosome 1were simulated according to the bovine genome and 50 K,770KSNP chip information Illumina bovine.One-step and two-step imputation strategies were proposed using two imputation programs Beagle and FImpute to fill SNP chips into the sequencing data.The results show that the one-step imputation strategy,directly imputing medium density SNP chips to sequencing data,generates lower accuracy than two-step imputation strategy.When the bull as a reference group,the imputation accuracy of daughter from two-step strategy is increased to 0.863 from 0.691 obtained by one-step strategy.Similarly,when using different scale cow as reference,the imputation accuracies of half sibs from two-step strategy are improved to 0.832~0.866 compared with 0.553~0.664 from one-step strategy.With enlarging the reference population,the imputation accuracy of SNP chips to sequencing data is further increased,and at the same time the genetic relationship also helps improve the imputation accuracy.the imputation accuracy of Beagle is worse than that of FImpute in one-step strategy and their gap is gradually narrowed with increasing the reference population size.However,the accuracies of genotype imputation of Beagle and FImpute are similar in the two-step imputation strategy.

关 键 词：动物遗传育种与繁殖 SNP芯片 基因型填充 测序数据 一步法 两步法 

分 类 号：Q811.4[生物学—生物工程]